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Yorodumi- PDB-8wim: Crystal structure of Jingmen tick virus RNA-dependent RNA polymer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wim | ||||||
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Title | Crystal structure of Jingmen tick virus RNA-dependent RNA polymerase (D307 construct) | ||||||
Components | Jingmen tick virus NSP1 | ||||||
Keywords | TRANSFERASE / RNA virus / flavi-like viruses / Jingmen tick virus / RNA-dependent RNA polymerase | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Jingmen tick virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Wang, X. / Jing, X. / Deng, F. / Gong, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase. Authors: Wang, X. / Jing, X. / Shi, J. / Liu, Q. / Shen, S. / Cheung, P.P. / Wu, J. / Deng, F. / Gong, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wim.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wim.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 8wim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/8wim ftp://data.pdbj.org/pub/pdb/validation_reports/wi/8wim | HTTPS FTP |
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-Related structure data
Related structure data | 8wilC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 71208.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Jingmen tick virus / Strain: YN-flaviV / Gene: segment 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta | ||||||
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#2: Chemical | ChemComp-MG / | ||||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / Details: potassium sodium tartrate tetrahyrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.84→50 Å / Num. obs: 58904 / % possible obs: 99.1 % / Redundancy: 6.7 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Χ2: 1.012 / Net I/σ(I): 9.6 / Num. measured all: 395284 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in-house model determined by SAD Resolution: 1.84→37.11 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→37.11 Å
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Refine LS restraints |
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LS refinement shell |
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